Negatively stained 50 S ribosomal subunits of Escherichia coli

Ribosomes are large nucleoproteins of approximately 3 X 10(6) Mr. In contrast to helical or spherical nucleoproteins (viruses) of similar size (which consist of several hundred small asymmetric units reproduced by symmetry), ribosomes are completely asymmetric; therefore, the amount of structural information (defined by the number of independent image elements) necessarily increases from about 10 to 20 to about 1000 to 2000 (at resolutions of the order of 2 nm). With present techniques, only stained single particles can be studied in the electron microscope. Our published work on the 30 S subunit and on the 50 S subunit has demonstrated that three-dimensional reconstructions of stained single particles show a great number of structural details that are reproducible if the particles have the same orientation. One of the main results of this paper is the final proof of this reproducibility from detailed comparisons of individual 50 S subunits and of independent averages over a few (3 to 5) particles in the kidney or crown orientation; in the latter case, even after a chemical modification. The 50 S subunit is non-uniformly stained along the optical axis. It displays a complicated, stain-filled channel-like structure, within which is approximately the partial volume expected for the RNA. The particle shows an irregular but reproducible boundary surface against the stain. At several sites, the channel structure protrudes to the surface. Since the secondary structure of the RNA is well known, one might try to locate it in the subunit after chemical identification of its surface contacts (the 3' end of 23 S RNA and the 3' end of the 5 S RNA have been localized). Most interesting is a groove on the surface, which might accommodate the mRNA.